Co-expression of neighboring genes in the zebrafish (Danio rerio) genome.

Tsai HK, Huang PY, Kao CY, Wang D - Int J Mol Sci (2009)

Bottom Line:
Our analysis shows that the proportion of highly co-expressed neighboring pairs (Pearson's correlation coefficient R>0.7) is low (0.24% approximately 0.67%); however, it is still significantly higher than that of random pairs.In particular, the statistical result implies that the co-expression tendency of neighboring pairs is negatively correlated with their physical distance.Possible mechanisms related to the neighboring genes' co-expression are also discussed.

ABSTRACTNeighboring genes in the eukaryotic genome have a tendency to express concurrently, and the proximity of two adjacent genes is often considered a possible explanation for their co-expression behavior. However, the actual contribution of the physical distance between two genes to their co-expression behavior has yet to be defined. To further investigate this issue, we studied the co-expression of neighboring genes in zebrafish, which has a compact genome and has experienced a whole genome duplication event. Our analysis shows that the proportion of highly co-expressed neighboring pairs (Pearson's correlation coefficient R>0.7) is low (0.24% approximately 0.67%); however, it is still significantly higher than that of random pairs. In particular, the statistical result implies that the co-expression tendency of neighboring pairs is negatively correlated with their physical distance. Our findings therefore suggest that physical distance may play an important role in the co-expression of neighboring genes. Possible mechanisms related to the neighboring genes' co-expression are also discussed.

f2-ijms-10-03658: Comparison of the co-expression levels of four gene distance patterns (50 kbp, 100 kbp, 300 kbp and 500 kbp sliding windows). In the upper figure, the Pearson correlation values of the four patterns and those of random pairs are used to construct their individual cumulative distributions. The lower table indicates the significance score of the KS test (p value).

Mentions:
Second, we also investigated the co-expression tendency of neighboring genes with various physical distances in the chromosomes. The sizes of the neighboring genes were identified using 50 kbp, 100 kbp, 300 kbp and 500 kbp sliding windows (see Materials and Methods for details). As shown in Figure 2, the co-expressions of four groups, 50 kbp (1699 pairs), 100 kbp (2987 pairs), 300 kbp (4945 pairs) and 500 kbp (5683 pairs) exhibit significantly higher co-expression levels compared to those of random pairs (p<0.01, one-sided KS test). The statistical results in Figure 2 also indicate a negative correlation between co-expression and distance, which implies that the physical distance between co-expressed pairs in a chromosome may have an effect on the co-expression level.

f2-ijms-10-03658: Comparison of the co-expression levels of four gene distance patterns (50 kbp, 100 kbp, 300 kbp and 500 kbp sliding windows). In the upper figure, the Pearson correlation values of the four patterns and those of random pairs are used to construct their individual cumulative distributions. The lower table indicates the significance score of the KS test (p value).

Mentions:
Second, we also investigated the co-expression tendency of neighboring genes with various physical distances in the chromosomes. The sizes of the neighboring genes were identified using 50 kbp, 100 kbp, 300 kbp and 500 kbp sliding windows (see Materials and Methods for details). As shown in Figure 2, the co-expressions of four groups, 50 kbp (1699 pairs), 100 kbp (2987 pairs), 300 kbp (4945 pairs) and 500 kbp (5683 pairs) exhibit significantly higher co-expression levels compared to those of random pairs (p<0.01, one-sided KS test). The statistical results in Figure 2 also indicate a negative correlation between co-expression and distance, which implies that the physical distance between co-expressed pairs in a chromosome may have an effect on the co-expression level.

Bottom Line:
Our analysis shows that the proportion of highly co-expressed neighboring pairs (Pearson's correlation coefficient R>0.7) is low (0.24% approximately 0.67%); however, it is still significantly higher than that of random pairs.In particular, the statistical result implies that the co-expression tendency of neighboring pairs is negatively correlated with their physical distance.Possible mechanisms related to the neighboring genes' co-expression are also discussed.

ABSTRACTNeighboring genes in the eukaryotic genome have a tendency to express concurrently, and the proximity of two adjacent genes is often considered a possible explanation for their co-expression behavior. However, the actual contribution of the physical distance between two genes to their co-expression behavior has yet to be defined. To further investigate this issue, we studied the co-expression of neighboring genes in zebrafish, which has a compact genome and has experienced a whole genome duplication event. Our analysis shows that the proportion of highly co-expressed neighboring pairs (Pearson's correlation coefficient R>0.7) is low (0.24% approximately 0.67%); however, it is still significantly higher than that of random pairs. In particular, the statistical result implies that the co-expression tendency of neighboring pairs is negatively correlated with their physical distance. Our findings therefore suggest that physical distance may play an important role in the co-expression of neighboring genes. Possible mechanisms related to the neighboring genes' co-expression are also discussed.